Even the latest PC/104 standard doesn’t include PCI-express. Check for yourself at http://www.pc104.org/
To get something in a small form factor for a reasonable price: go microATX. If that is still too big: go mini-itx http://www.mini-itx.com/ . The latest VIA boards have PCI express. But the VIA Eden processer by no means has the performance of a Core 2 duo. And to run the top of the line GPU on one of those boards, you will need a power supply several times larger than the mainboard :) (unless you plan on running the system on a DC-DC power supply)
I’m not aware of any embedded type systems with the kind of performance you are looking for. Usually embedded systems = low power and low performance because they are built to perform a simple specific task and don’t need all the wasted horsepower it takes to run windows Vista.